AMBER Archive (2002)

Subject: Re: Amber 7 and 6 topology files.

From: James W. Caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Mon Sep 30 2002 - 10:41:25 CDT

The most common cause of this "error" is extra (blank) lines
in the -c file (at least that's how I trigger it). Use an
editor to look at both your -p and -c files and make sure
there are no stray blank lines at the end.

jim

On Mon, 30 Sep 2002, Miguel de Federico wrote:

> I have been told that if I use amber 7, I can use the new2oldparm for
>having amber 6 topology files which I can use with sander provided with
>amber 6.
>
> If i'm not wrong, the usage is: new2oldparm <newamber7 > oldamber6
>
> I have done so, but sander still doesn't works. Here is the output for
>a simple minimisation.
>
> Could anybody help me about this?
>
>
>
> -------------------------------------------------------
> Amber 6 SANDER Scripps/UCSF 1999
> -------------------------------------------------------
>
>| Mon Sep 30 16:56:28 2002
>
> [-O]verwriting output
>
>File Assignments:
>|MDIN : 001min10k.in
>|MDOUT: AdA200min.out
>|INPCR: ../../6leap/AdA200.crd
>|PARM : ../../6leap/zAdA200.top
>|RESTR: AdA200min.rst
>|REFC : refc
>|MDVEL: mdvel
>|MDEN : mden
>|MDCRD: mdcrd
>|MDINF: AdA200min.inf
>
>
> Here is the input file:
>
>Optimizacion en 10000 ciclos
> &cntrl
> ntb=1, imin=1, maxcyc=10000,
> ntx=1, scee=1.2
> &end
>-------------------------------------------------------------------------------
>
>Optimizacion en 10000 ciclos
>
>
>
> 1. RESOURCE USE:
>
> getting box info from bottom of parm
> getting new box info from bottom of inpcrd
> peek_ewald_inpcrd: SHOULD NOT BE HERE
>
> 

-- 

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James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-502-1411  
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